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revision 1.122 by jmc, Thu Jan 23 15:35:48 2003 UTC revision 1.595 by heimbach, Thu Dec 22 21:16:17 2005 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
8      affects output (@ truncation level) of exp. plume_on_slope ; updated.
9    o fix the pickup behavior for obcs in combination with ptracers
10    o fix a bug in ptracers_external_fields_load
11    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
12      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
13    o transfered surface NH pressure to eta field (if exactConserv).
14    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
15         and update lab_sea output.txt file.
16    o completing 3-dim. relaxation code: additional term
17         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
18      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
19      * At compile time, in "EXF_OPTIONS.h" set
20          #define  ALLOW_CLIMTEMP_RELAXATION
21          #define  ALLOW_CLIMSALT_RELAXATION
22      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
23          tauThetaClimRelax3Dim = 15552000.0,
24          tauSaltClimRelax3Dim  = 15552000.0,
25      * 3 cases:
26          1) Use a constant-in-time 3-dim. field
27          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
28          3) Real-time relax. to time-evolving prescribed field
29    o Adding Laplacian-type smoothness constraint on
30      initial and boundary (forcing) controls (ic, bc)
31      * enable at compile-time via
32        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
33      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
34      * Absolute scale somewhat unclear so far
35      * no area weighting was included since no other cost term does so far
36    
37    checkpoint57y_post
38    First step for a NLFS adjoint
39    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
40    o new init. routines for calc_r_star, calc_surf_dr
41    o still need to deal with ini_masks_etc
42    o testreport seemed happy
43    checkpoint57y_pre
44    
45    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
46    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
47    o add new offset feature to offline pkg (plus minor cleanup)
48    o cfc fixes for final year of integration
49    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
50      be in GCHEM_OPTIONS).
51    
52    checkpoint57x_post
53    o fix testreport Pb in multiple test experiment.
54    o cleanup our namelist syntax in verification:
55      - make it more F95 standards compliant (some work still needed)
56      - allows the vast majority of our tests to work with gfortran
57    o Non-Hydrostatic:
58     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
59     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
60    o Allow to apply AB on T,S rather than on AB(gT,gS):
61     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
62     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
63       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
64     - need a "clever" read_pickup to restart from the other AB formulation
65    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
66    o remove some unused variables (reduces number of compiler warnings)
67    o adjoint
68      * Disable useVariableViscosity for adjoint for time being
69        (there are a number of extensive recomputations)
70      * Initialize certain variables needed for adjoint
71    
72    checkpoint57w_post
73    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
74                 fix the singleCpuIO RS version of MDSWRITEFIELD
75       and add a WARNING if using globalFiles=T with multi-processors.
76    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
77      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
78    o tracer advection scheme:
79      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
80       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
81       was not very convenient).
82      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
83       (further tests needed for the implicit DST & Flux-Limiter schemes).
84    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
85      and sRef for convenience, handy, when you want to initialize
86      ptracers in a large domain with a constant non-zero value. Also,
87      untangle ptracers_init.F a little.
88    
89    checkpoint57v_post
90    o change dome exp. to use variable viscosity in side-drag terms.
91    o remove all the files from the cfc_offline test since they are now
92      incorporated into tutorial_cfc_offline which has been producing
93      identical results for a few days of testing
94    o add new parameter: sideDragFactor to enable half-slip-side BC
95      and change side-drag S/R to use viscosity from mom_calc_visc
96      (can switch back by setting sideDragFactor=0.); affects results at
97      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
98       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
99    o vorticity & strain are now computed without masking, to account for
100      no-slip-side BC in variable viscosity calculation ; mask is applied
101      anyway later on, before computing advection/coriolis terms.
102    o modify exp4 to test new obcs support for reading from external files
103      and for passive tracers
104    o fix behavior of ptracers_monitor when monitor output is written to a
105      netcdf-file; still not independent of monitor.F (writes in the same
106      file).
107    o change default value of tRef (put a uniform, meaningful value for ocean
108      & atmos) and initialize sRef (was missing, as Martin mentioned).
109    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
110      to be proportional to enstrophy dissipation length.  Thus,
111       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
112      This is now consistent with Smagorinsky and with the manual.
113    
114    checkpoint57u_post
115    o OBCS and PTRACERS: add open boundary support for passive tracers
116      - either use homogenous (pseudo) v.Neumann conditions or prescribe
117        OB-values from file; this is not different from the way theta and salinity
118        are treated
119      - however, Orlanski-radiation conditions are not supported, and the model
120        will stop if you use pTracers and Orlanski at the same time.
121      - beefed up the rountine obcs_external_fields_load: now only those open
122        boundary values are overwritten with values from files for which there
123        are really files, otherwise the OB-fields remain untouched. This makes
124        it possible to use different OBs at different ends of the domain (as
125        with EXF)
126    o reduce number of exch calls in shap_filt (s2).
127    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
128      truncation level) 4/5 MLAdjust test results (11&12 digits match).
129    
130    checkpoint57t_post
131    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
132    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
133      same truncation, independent of the face number: affects affects several
134      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
135    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
136      note that biharmonic viscosity + no-slip was not tested in any experiment.
137    o fix bug in non-linear free-surf side-drag ; generate new output for
138      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
139    o make mnc honor the writeBinaryPrec flag for most kinds of output
140    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
141    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
142      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
143    o add brackets in multi-terms sum to get same truncation, independent of
144      the face number (manage to get exactly same value of gU,gV at the cs-edge)
145      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
146    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
147      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
148      a maximum grid-scale Reynolds number.  Also, changes all length calculations
149      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
150      Suggested values of viscosity parameters found in mom_calc_visc.
151      Many new viscosity diagnostics available.
152    
153    checkpoint57s_post
154    o Add clearing-house for viscosity calculations, mom_calc_visc and
155      correct numerous bugs in LeithD and Smagorinsky discretizations.  
156      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
157      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
158      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
159      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
160      The Strain-Tension form is now called with useStrainTensonVisc=.true.
161      ViscAhStrain and viscAhTension are now retired.
162    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
163    o In response to JMC's bug report, genmake2 now ignores any soft-links
164      that it finds in the *current* directory when searching for files.
165      Soft-links found in any other source directories will still work as
166      they did before.
167    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
168      a C routine to unlimit the stack size
169    o mnc-ify pkg/aim snapshot vars
170    o mnc-ify pkg/land as requested by Daniel
171    o various changes to mnc including:
172      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
173      - output can now be grouped so that all files within a group
174          change the ITER portion of their names in lock-step together
175      - can now read ("global") PER-FACE (in addition to PER-TILE) files
176          and works with both EXCH1 and EXCH2 (but needs more testing)
177      - writing works for all verification test cases w/ g77 on Linux
178    
179    checkpoint57r_post
180    o make MNC variable initialization happen earlier
181    o add diagnostics for (almost) each term of the momentum Eq.
182    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
183    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
184    o remove MINIMAL_TAVE_OUTPUT option ;
185      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
186    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
187      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
188    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
189    o add time-dependent SST, SSS control
190    o cost terms in ecco/ modularized (new cost_generic.F)
191    o cost_averages routines are modularized (new cost_averagesgeneric.F)
192    o new infrastructure for seaice model vs. obs misfits in seaice/
193      * driver from the_main_loop.F is seaice_cost_driver.F
194      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
195      * gradient check in Exp. 6a of natl_box_adjoint/
196    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
197      (see README file)
198    
199    checkpoint57q_post
200    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
201    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
202      - bug was reported by Jean-Michel and Ian Fenty
203    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
204      update exp. cpl_aim+ocn output.
205    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
206      Needed for high-res. runs with large global files
207      to be able to limit tapelev size
208    o Changed some tests for adjoint:
209      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
210      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
211      * global_ocean.90x40x15/ back to default 3-level checkpointing
212    o Modifications to enable scripted COMMON to MODULE conversion
213      * verification/OpenAD/code/ has necessary scripts and description;
214      * converts, compiles and runs successfully;
215    
216    checkpoint57p_post
217    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
218    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
219      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
220    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
221    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
222      (was already the case for dissipation with mom_vecinv,
223       and also the case for grad.PhiHyd when staggered-timeStep)
224      This will allow to put dissipation out-off the AB time-stepping.
225     Unfortunately, affects truncation error. Update output of exp. that "fails"
226      (cg2d matching number) and leave the others for later: front_relax(10),
227      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
228      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
229    
230    checkpoint57o_post
231    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
232      (2) its ready to be documented during the 20050801 DocFest
233    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
234      for ideal_2D_oce and lab_sea on linux_ia32_g77
235    o set to #undef CTRL_SET_OLD_MAXCVARS_30
236      in global1x1_tot/code_seaice_adj to access indices 32, 33
237      (worth another tag)
238    
239    checkpoint57n_post
240    o adding precip control xx_precip 32
241    o adding swflux control xx_swflux 33
242    o Replacing 10 forcing penalty cost routines by 1 generic.
243    o Implementing partitioning in time-mean and variable adjustment
244      for atmos. state.
245    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
246    o in natl_box_adjoint:
247      * updated exp 1 to 10
248        (but does not have time-mean vs. variable split results yet)
249    o updated global1x1/*_seaice_adj/
250      to incorporate latest changes
251    o enable useSingleCpuIO for mdsio vector routines
252      (applies in particular to tapelev I/O)
253    o removed inefficient K-loop in all active_file*control*.F
254    
255    checkpoint57m_post
256    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
257      and advect_cs (use EXCH-2 and standard cs-32 grid files).
258    o pkg/exch2: filling of face-corner halo regions is optional
259      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
260    
261    checkpoint57l_post
262     tag before updating tutorials (pre-release-2)
263    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
264       for output and interpolation of input fields onto model grid)
265    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
266       Affects results of exp. rotating_tank ; update output.txt.
267    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
268          and taking the square quantity and/or using a fraction-weight field.
269    o fix aim_diagnostics_init.F mate numbers.
270    o add mnc output capability to diagnostics/diagstat and update
271      our cvsignore files for the ACSII output generated
272    
273    checkpoint57k_post
274    o lab_sea now uses diagnostics package and provides a suite of
275      new EXF diagnostics output.
276    
277    checkpoint57j_post
278    o exf
279      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
280        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
281        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
282      * extended diagnostics output
283        - now includes all EXF variables
284        - hs, hl moved to common block
285        - separate S/R for diagnostics, called after ctrl vector is added
286        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
287        - EXFqnet contains true Qnet (i.e. includes qsw)
288      * updated verif. lab_sea, global_with_exf
289      * Rearranging hflux (exf_mapfields -> exf_getforcing)
290        to ensure that diagnostics sees a true EXFqnet
291    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
292    o diagnostics pkg: change pointers so that 1 diagnostic can be used
293      several times with different frequencies.
294    o mnc-ify the thsice package as requested by Daniel Enderton
295      - the monitor--MNC output needs work
296      - many attributes need to be added (most are currently blank)
297    o mnc-ify theaim_v23 package as requested by Daniel Enderton
298      - many attributes need to be added (most are currently blank)
299    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
300    o add Sadourny like discretization to the 4th.O vorticity advection scheme
301    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
302      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
303         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
304    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
305     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
306    
307    checkpoint57i_post
308    o Diagnostics package was changed: diagnostic allocation is now deactivated
309      by setting an empty file name in the namelist (used to be by setting 0 frequency)
310    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
311      add 1rst Order upwind vertical Shear.
312    o add a quick fix for A/B checkpointing in OFFLINE mode
313    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
314      end-run around the C/Fortran linking horror in eesup/src/timers.F
315    o added pkg/runclock: allows user to terminate run based on wall clock
316    o added non-hydrostatic scaling parameter: nh_am2
317    o pkg/my82: futile attempt to make results compiler-independent by adding
318      some "_d 0", etc. no effect.
319    o for mnc output, fill the 'T' coordinate var with myTime and create a
320      separate 'iter' variable for iteration count
321    o pkg/diagnostics:
322      add new capability: output of Global/Regional & per-level statistics ;
323      tested against monitor output (including land & thSIce) on various exp.
324    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
325    
326    checkpoint57h_done
327      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
328      data.diagnostics, data.gchem, data.ptracers) is done.
329    
330    o pkg/diagnostics: prepare for Global/Regional statistics.
331      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
332    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
333      and rename it: DIFFERENT_MULTIPLE
334    
335    checkpoint57h_post
336    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
337    o pkg/diagnostics: change output frequency, now in seconds (instead
338      of Nb of iterations). This requires to change data.diagnostics.
339    checkpoint57h_pre
340    
341    o in mnc, let the user create the output dir if both mnc_outdir_date
342      and mnc_outdir_num are false
343    o add fflags() to pkg/diagnostics which allows one to specify, on a
344      per-file basis, the file precision [default behavior is unchanged]
345    o added diagnostics to pkg/kpp, including computation of mixed layer
346      depth based on a temperature/density criterion
347    o updated verification/natl_box to test the new pkg/kpp diagnostics
348    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
349    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
350    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
351      not mnc -- this mistake was found by JMC and is now corrected
352    
353    checkpoint57g_post
354    o add Adams-Bashforth 3rd Order time stepping:
355      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
356      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
357    checkpoint57g_pre
358    
359    o make lambda[Theta,Salt]ClimRelax spatially varying
360      (default remains spatially uniform constant based on tau)
361    o added new control variables
362      * init. uVel, vVel, etanN
363      * lambda[Theta,Salt]ClimRelax
364    o separate masks used for ctrl_pack/unpack 'from write_grid' output
365      (suggested by G. Forget)
366    
367    checkpoint57f_post
368    o add parameter "baseTime" = model base time = time at iteration zero
369      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
370      account for baseTime shift
371    o move Coriolis arrays from PARAMS.h to GRID.h
372    checkpoint57f_pre
373    
374    o mnc-ifying the seaice package
375    o introduced an alternative length scale calculation for use in the limiting
376      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
377    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
378    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
379      as well as grad(vort3).  Made it compatible with both approximate form
380      for the cubed sphere and full form of these gradients.  Added flag
381      useFullLeith to select between approximate and full form.  
382    o add "d0" in getcon.F to reduce differences between compilers/platforms
383      update output.txt of exp. fizhi-gridalt-hs
384    o change port_rand funtion to allow to set the seed.
385    o fix obscure MNC bug involving conversion between reals and integers
386      - it caused no problems with certain (eg. gcc, ifc) compilers but the
387        new version is now more standards-compliant
388    o adjoint-related modifications
389      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
390      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
391      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
392    
393    checkpoint57e_post
394    o Adding eddy stress controls a la Ferreira et al.
395    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
396    
397    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
398      update output.txt of exp. fizhi-gridalt-hs
399    o add more "Z" dimensions and associated coordinate vars to MNC
400    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
401    o parameter calendarDumps: when set, approximate months (30-31 days) and years
402      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
403      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
404      months and years.  Requires pkg/cal.
405    o diagnostics: add pickup functionality
406      - off by default for backwards compatibility
407      - current version only uses MDSIO -- MNC will be added
408    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
409    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
410    
411    checkpoint57d_post
412    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
413    o modify verification/ideal_2D_oce so that it tests the creation of mnc
414      output from the diagnostics package
415    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
416    o make genmake2 more portable by using ".$FS" instead of ".f" for more
417      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
418    o add coordinate variables to the MNC output from the diagnostics package
419    o change MNC-flags default value: true when useMNC=TRUE
420    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
421      the ability (off by default) to read the grid information using MNC
422    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
423    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
424    o do snap-shot diagnostics at the middle of the time-interval (instead of
425      at the end).
426    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
427      new test for AIM with thSIce + slab-ocean
428    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
429    o move state variable diagnostics to the beginning of the time step ;
430      (note: still needs some work specially for snap-shot diagnostics)
431      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
432    
433    checkpoint57c_post
434    o Change testing option (-ieee) to get closer agreement between g77 & ifort
435    o generate new output.txt files on faulks with g77 & the new -ieee option
436    checkpoint57c_pre
437    
438    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
439      update output.txt of exp. global_ocean.90x40x15
440    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
441      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
442    o add saltFlux(+File) forcing capability with periodicExternalForcing
443    o allow to use pkg diagnostics for GM-Redi & ThSIce output
444    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
445    o improvements for the MNC output from DIAGNOSTICS:
446      - correct handling of the unlimitied dimension
447      - all dims now have associated coordinate variables
448      - variables located at U, V, and Corner ("Z") points are now written
449        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
450        *all* data points are output
451    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
452    o added pkg/seaice/seaice_monitor.F
453    o mdsio_readfield.F can now read files visible only to master MPI process.
454    o pkg/seaice: some test code for ice-modified ocean stress
455    o exf_getffields interpolation defaults to bilinear for all scalar forcing
456      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
457      spurious negative numbers for precipitation and humidity.  Will cause
458      some small numerical differences for integrations using pkg/exf/exf_interp.F.
459    o pkg/ctrl/
460      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
461        May be enabled via doPackDiag
462      *  introduce z-scaling of
463         + gradient (doZscalePack) and
464         + control (doZscaleUnpack)
465    o pkg/mdsio/
466      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
467      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
468    
469    checkpoint57b_post
470    o simplify options in diagnostics_fill arguments (remove weird combinations)
471    o fix MNC coordinate variables so that they now contain per-face index
472      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
473      general, EXCH2 grids are only aligned to a "local" coordinate system
474    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
475    o Implement instantaneous output within pkg diagnostics:
476      setting a negative frequency in data.diagnostics produces
477     "snap-shot" output (as opposed to time-average if freq > 0)
478    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
479      NOTE: change ptracer diagnostics name: use 2 characters to work with
480            more than 9 tracers. Add also diagnostics of advect & diffus flux.
481    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
482      becomes the coordinate variable for the 'T' dimension
483    o add CF-style coordinate variables to MNC
484      - just a first cut:  numbers are meaningless on the cubesphere and
485        missing along the T axis but otherwise it works!
486    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
487    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
488    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
489      this is based directly on what the model compute, so that the content of
490      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
491    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
492    o clean up build options files for SunOS, in particular
493      - remove -traditional from xmakedepend
494      - change -xarch=v9 to -xarch=native for f77
495      - restore use of make (not gmake)
496      - add CC=gcc if using g77
497    o changes per discussion of AM, JMC, & EH3 today:
498      - move redundant "grid" variables out of "state" -- in preparation of
499        creating proper CF-style coordinate variables and in recognition
500        that any/all grid variables can be easily copied (eg. w/NCO) from
501        the grid files into any of the other NetCDF files
502      - *always* output grid variables with MDSIO (this will eventually be
503        changed)
504      - output MNC grid file if useMNC is true
505    o every instance of _END_MASTER() has been found and replaced with
506      _END_MASTER( myThid ) in order to satisfy certain picky Sun
507      preprocessors
508    o re-arrange diagnostics pkg initialisation:
509     - allow each package to extend the available diagnostics list
510     - add some checking and fix small problems (multi-threaded, ...)
511     - new S/R diagnostics_fill (replace fill_diagnostics):
512       look through the short list of active diag. (instead of the long list)
513       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
514    
515    checkpoint57a_post
516    o this set of changes restores TAMC compatibility
517      tested for global_ocean.90x40x15 adjoint on trough
518      (what a pain)
519    
520    checkpoint57a_pre
521    o some modifs in tools/build_options for sunos
522    o call ctrl_pack for ctrl at end for optimcycle=0
523    
524    checkpoint57
525    o add horizontal bi-harmonic viscosity for vertical velocity
526      - new parameter viscA4W (defaults to viscA4)
527      - affects only non-hydrostatic code
528      - to be done: no-slip lateral boundary conditions
529    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
530    o implement Implicit Vertical advection for pTracers
531    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
532      (implemented also for implicit vertical diffusion & advection)
533    o OBCS: extend application of tracer open boundary conditions
534      to a strip beyond the boundary of width Olx/Oly
535    o add call monitor to TAF set of required calls (flow directives)
536      and include in natl_box_adjoint
537    o untangle a few ifdefs related to cost, ctrl, autodiff
538      untangel a few ALLOW_ECCO_OPTIMIZATION
539    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
540      (theta2, salt2 in ecco_cost_weights)
541    
542    checkpoint56c_post
543    o OBCS as control variables
544      - update ctrl_ad_diff.list, obcs_ad_diff.list
545      - remove balance of obcs controls from default
546      - fix index bug nobcs in ctrl_init
547      - fix dummy fields filen in ctrl_pack
548      - add dummy weights for obcs
549    o lsopt: comment out fort.94 output
550    o optim:
551      - remove unnecessary header files
552      - adjusted namelists
553      - add xerbla.F to Makefile
554    o exf:
555      - multiple modifications of exf_check_range
556      - unit change in exf_init_runoff from [m/year] to [m/s]
557    o mdsio:
558      - i/o-vector change debugLevel from debLevA to debLevB
559    
560    checkpoint56b_post
561    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
562      is called from DO_THE_MODEL_IO
563      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
564      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
565      - clean up PTRACERS_WRITE_TIMEAVE a little
566    o add another verification experiment that tests both the cfc-pkg and
567      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
568      reactive tendencies treated inline with regular timestepping
569    o testreport previously did a lousy job of comparing small numbers, so
570      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
571      implemented in the little c-progam tmp_cmpnum.c which is embedded in
572      testreport.
573    o ptracers_monitor: bug fix for MPI
574    
575    checkpoint56a_post
576    o GCHEM: finish reorganizating the package
577      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
578        (introduces another 3D-array for each passive tracer, but only if
579        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
580        gchemTendency is not needed because the timestep is done separately)
581      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
582      - GCHEM is now---more or less cleanly---separate from PTRACERS
583      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
584        so clear to me how that should be done in a general way.
585    o CFC: improve formatting of output in CFC_ATMOS
586    o PTRACERS:
587      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
588        that ALL experiments with ptracers enable can be checked. This makes
589        GCHEM_MONITOR obsolete.
590      - include a runtime parameter PTRACERS_monitorFreq that defaults to
591        monitorFreq
592      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
593    o add PTRACERS (PTR0[1-5]) to testreport output
594    o exf_check_range:
595      * default changed to .TRUE.
596      * will check values for niter0 if debLevA, every timestep if debLevB
597      * STOP in exf_check_range if 'out of range'
598      * range chosen generous to allow for potential extema
599      TBD: a version with stricter range
600           permitted range would be runtime parameters
601    o GMredi:
602      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
603      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
604      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
605    o GCHEM:
606      - move call to GCHEM_FORCING_SEP, so that it is now called before
607        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
608      - introduced a useGCHEM runtime flag and applied it everywhere.
609      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
610        this flag is now only visible within GCHEM-pkg routines.
611      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
612        be replaced by a 3D array that is computed before thermodynamics; for
613        this, the tracer ID iTracer had to be included into the parameter list
614        of ptracers_forcing
615      - set up forward_step to call gchem_forcing, that will replace
616        gchem_forcing_int in ptracers_forcing
617      - cleaning up
618    o small cleaning of exch2: remove files that are also in eesupp/src
619    
620    checkpoint56
621    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
622    o mnc: cleanup "full" files--fixes out-of-memory problem
623    o ECCO-GODAE
624      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
625      * fully merged and updated from SIO code
626        windstress sign change affects
627        - exf_inscal_[u/v]stress
628        - sign of xx_tau[u/v] adjustments
629        - signs in cost_scat
630      * ctrl_get_gen: avoid update of tau[u/v] for first few days
631      * natl_box_adjoint updated and compressed
632      * 2-level checkpoint switch added
633        (tested in EXP. 1 of natl_box_adjoint)
634      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
635    o SVD
636      * first complete, non-hacked version for SVD calculations
637      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
638        performed via direct access files admtlm_vector.it????
639        (via ctrl_[un]pack)
640      * optimcycle is used for ARPACK iteration counter
641        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
642      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
643        and add linear transforms where necessary
644      * controls are initial/final SST, SSS (can be extended; need to check
645        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
646    o mdsio: filename info to both stderr, stdout
647    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
648      from sign change
649    
650    checkpoint55j_post
651    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
652      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
653    o add consistent build directories and .cvsignore files to verification
654    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
655    o make all subroutines 30 or less characters in length for certain older
656      compilers to work (a thorough search only turns up two routines in
657      pkg/ptracers)
658    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
659      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
660    
661    checkpoint55i_post
662    o change arrays for total vertical diffusivity (2.D if explicit,
663      3.D if implicit) ; each ptracer uses its own background value.
664    o added mnc/NetCDF output capability to ocn_compon_interf
665      - added bits to verification/cpl_aim+ocn so that it can run on
666        ITRDA and other clusters without the mpirun "-wd" option
667    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
668      configuration
669    o give MNC the ability to create additional files rather than
670      exceeding a specified file size limit "MNC_MAX_FILESIZE"
671      - the default is just less than 2GB which is a practical limit
672        on many systems
673    o Compute the non-local term using either KPP vertical diffusivity (=default)
674       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
675    
676    checkpoint55h_post
677    o add verification test "vermix"
678    o remove all the *_ioinc flags and replace with the single global
679      outputTypesInclusive flag
680    o allow to set a vertical profile of vertical diffusivity for T & S
681    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
682    o useMNC moved from data.mnc to data.pkg
683    
684    checkpoint55g_post
685    o Renaming carbon AD experiments to comply with testreport conventions
686    o Updating adjoint of Held-Suarez hs94.1x64x5
687    o Fixing directives for non-ECCO forward_step, after ECCO directives
688      have been fixed to avoid recomp. of do_oceanic_phys
689      Works well for global_ocean.90x40x15,
690      but recomp. issue remains for carbon
691    o Updating adjoint output for natl_box_adjoint after
692      pkg/ecco has been modified (see taga c55d_post)
693    
694    checkpoint55f_post
695    o rename to timeave_init_fixed
696    
697    checkpoint55e_post
698    o some delicate re-shuffle of store directives to avoid one
699      extra call of do_oceanic_physics
700      affects ecco_the_main_loop.F, do_oceanic_physics.F
701      checkpoint_lev1_directives.h
702    o NB: this may break global_ocean adjoint temporarily,
703      but it is clear how to fix it. Will do later, need this now.
704    
705    checkpoint55d_post
706    o ECCO specific cost function terms (up-to-date with 1x1 runs)
707    o ecco_cost_weights is modified to 1x1 runs
708    o modifs to allow observations to be read in as
709      single file or yearly files
710    o enable to read exf forcing fields as either
711      single file or yearly files (flag useExfYearlyFields)
712    checkpoint55d_pre
713    
714    o switch between 2-level and 3-level checkpointing
715    o add ability of MNC to write local and "partial" (eg. 2D slices where
716      the full 3D field is never actually stored) arrays to NetCDF files
717      with the correct (that is, the complete multi-dimensional) set of
718      array indicies
719      - used in mom_vecinv() to write the diagFreq output
720      - tested (demonstrated) in verification/aim.5l_cs
721    o further mnc-ification
722      - add verification/lab_sea to the list with mnc setups
723      - fix undefined mnc v-names in cd_code
724      - add kpp to mnc output (both snapshot and timeave)
725    o non-hydrostatic code
726      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
727        in calc_gw.F
728      - defaults to viscAh
729      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
730        friction or Leith) in non-hydrostatic mode, as long as there is
731        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
732    o pkg/cost
733      extend simple cost functions to treat time mean quantities
734      (T,U,V) via cost_accumulate_state from cost_tile
735    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
736        be 2 times larger than the minimum size the advection scheme requires.
737        now get a perfect conservation of salt in advect_cs test-exp (updated)
738    o GGL90 (Gaspar's TKE mixed layer)
739      - add horizontal diffusion of TKE, requires exchanges in
740        do_fields_blocking_exchanges, horizontal diffusivity is zero by
741        default. In OPA there is no horizontal diffusion of TKE but the
742        mixing coefficients are computed from a horizontal average of TKE of
743        6 points or so. I think that diffusion has a little more physical
744        justification.
745      - clean up ggl90_calc in the hope of reducing memory usage (this hope
746        was in vain)
747      - mask tke-variable in ggl90_init
748    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
749    o fix biharmonic diffusion on CS-grid.
750    o more obcs stuff
751      - added obcs_external_fields_load as an alternative to the EXF-pkg option
752        for reading boundary values. This routine is called from
753        obcs_prescribe_read
754      - updated obcs_check
755      - changed sponge layer relaxation parameter units for days to seconds
756      - turned off sponge layer by default
757      - changed argument list of OBCS_CALC to myTime+deltaTclock
758      - fixed about 35 bugs in obcs_external_fields_load
759    
760    checkpoint55c_post
761    o obcs stuff
762      - new runtime flags useOBCSprescribe, useOBCSbalance
763      - re-arranged obcs_calc
764      - moved exf_getobcs to obcs_prescibe_read
765        obcs_prescibe_read is called after ORLANSKI stuff
766        and independent of it (executable can contain all).
767      - updated obcs_check
768      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
769        These may be necessary only if tangential velocities are
770        prescribed at OB, not sure, needs testing.
771    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
772      which simplifies the calls and passes the ifc check-bounds test
773    
774    checkpoint55b_post
775    o add a 2D scalar, Z location, exchange_2 routine.
776    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
777      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
778      affects advect_cs results (for the wrong reason): update output.txt
779    o use a more standard discretization for biharmonic viscosity ;
780     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
781      affects results of dome set-up: update output.txt
782    o fix gad_advection.F (CubedSphere part), back to version 1.23
783    o fix bug in mom_vi_del2uv.F (CubedSphere part).
784    
785    checkpoint55a_post
786    o merged code to
787      * prescribe/read time-dependent open boundaries
788        (works in conjunction with exf, cal)
789      * sponge layer code for open boundaries
790      * each boundary N/S/E/W now has its own CPP option
791        (healthy for the adjoint)
792    
793    checkpoint55
794    o up-to-date adjoint of previous breaks
795      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
796      - global_ocean_ebm: adjoint still needs fix (TLM ok)
797      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
798      - carbon: * remove tr1-related adjoint verification
799                * add ptracer as control variable
800    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
801      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
802    
803    checkpoint54f_post
804    o in verification/carbin/ remove experiment related to
805      ALLOW_PASSIVE_TRACER (array tr1 etc)
806      code_ad/ input_ad/ results_ad
807    
808    o add two new packages
809      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
810        + subject to optimization (memory)
811      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
812        + subject to reordering (many GOTOs in the original code)
813        + so far opps is called for every (i,j) point, and then operates in
814          the vertical; one may want to reorder the scheme in order operate in
815          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
816          fields)
817    o overhaul of IO so that we now have flags for MDSIO and/or MNC
818      - all verification tests compile and run with linux_ia32_g77
819      - defaults are compatible with current input files--nothing
820        should change if you were not previously using MNC
821      - MNC output has been added in numerous places (eg. timeave)
822        but there are still a few writes not yet do-able with MNC
823        (this is in progress)
824      - flags now allow for either/or/both use of MDSIO and MNC and
825        documentation will soon follow
826      - numerous small formatting cleanups for ProTeX
827    o add version info (via BUILD_INFO.h) to MNC and stdout
828    
829    checkpoint54e_post
830    o add two new packages
831      - pp81 (Packanowski and Philander, 1981), Richardson number and
832        stratification dependent mixing
833      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
834      - these scheme operate in a similar manner as KPP (without ghat, of
835        course), however there is only one diffusivity that is used for both
836        temperature and salinity (and passive tracers)ç
837    o add offline package
838    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
839      provided by Stephanie Dutkiewicz
840    o genmake2: add ability to search for C compilers and cleanup test output
841      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
842    
843    checkpoint54d_post
844    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
845    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
846      leading to additional shift by 5 days each year of integration
847       (i.e. leading to considerable offset over the years)
848    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
849    o start with no AB and no initial filtering (staggerTimeStep):
850      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
851    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
852      (external loading & cpl import/export stay in forward_step.F)
853    o update coupling interface to work with new staggerTimeStep
854    o change MDSIO ptracers_pickup.
855    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
856    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
857    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
858    
859    checkpoint54c_post
860    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
861      this affects (truncation error) output.txt of test-exp:
862       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
863    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
864    o change Qnet to always be the net heat flux, (+upward).
865      affects (truncation error) output of natl_box exp.: updated
866    o define the max number of passive tracers in PTRACERS_SIZE.h
867    o start to test mnc routinely in exp0
868    o add sea-ice loading (sIceLoad) as a new forcing field.
869    
870    checkpoint54b_post
871    o add testreport "-j JOBS" option for parallel builds (tested and pretty
872       impressive on Altix and Opteron systems)
873    o diagnostics can now write NetCDF files through the mnc package
874    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
875    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
876    o staggerTimeStep & NLFS: rescale T & S surface tendencies.
877      affects (truncation error) output of lab_sea & natl_box exp.: updated
878    o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
879    
880    checkpoint54a_post
881    o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
882    o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
883    o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
884    o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
885      + internal_wave (shift in writing cg2d_ini_res)
886    checkpoint54a_pre
887    
888    o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
889      - modified verification/lab_sea and natl_box_adjoint accordingly
890    
891    checkpoint54
892    checkpoint53g_post
893    o prepare splitting of thermodynamics: store convect.counter in common block
894    o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)
895      output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
896    o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
897    o new parameter "nShapS": allow to treat differently S from T (nShapT)
898    o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
899    o restore adjointability
900    
901    checkpoint53f_post
902    o modifications that affect AIM experiment results (update output.txt):
903      - no advection of S at top interface Nr (pkg/generic_advdiff)
904      - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
905    o AIM pkg:
906      - include stability function into surf.Flux derivative relative to Tsurf
907      - calculate clear-sky radiation & surface temp. change (for diagnostics)
908    
909    checkpoint53e_post
910    o merged cylindrical coord configuration
911    o added rotating_tank experiment
912    checkpoint53e_pre
913    
914    checkpoint53d_post
915    o faulks upgraded: re-generate output.txt that have changed:
916       global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
917    o Added Bryan and Lewis, 1979, vertical diffusivity profile
918    o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing.
919    o added Sadourny discretization of Coriolis
920      - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
921      - re-enabled use of omega3 (useAbsVorticity)
922    o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
923      vector-invariant equations
924      - note: does *NOT* yet use same variable visc. for no-slip BC's.
925    o recoded the lateral boundary conditions for non-hydrostatic w, this time
926      hopefully without new bugs
927      - still to do: biharmonic friction for non-hydrostatic w
928    o bug fix for mom_*_sidedrag: rA -> rAs,rAw
929    o regenerated output for global_ocean_ebm (using -ieee)
930    o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
931      of mom_common/
932      - simple re-arrangement of instructions within computing loop
933    checkpoint53d_pre
934    
935    checkpoint53c_post
936    o new version of coupler for AIM+thSIce and Ocean models
937     - new fields (SSS,h_MixLayer ...) are exchanged through the coupler
938     - land: change Evaporation of snow
939     - aim with thSIce: fix bug in snow-precip.
940    o changes to calc_gw.F
941     - bug fix for w^2 term near the bottom boundary
942     - (hopefully) improve the lateral slip boundary condtions for use with
943        partial/looped cells
944      - because the bug fix changes two verification experiments anyway (exp5
945        and plume on slope), change the lateral boundary condition from half slip
946        to the value of no_slip_sides
947    o ebm package wasnt quite up to the parallel task. Fixed that.
948    o Adjoint of EBM package + verification
949      * TLM OK
950      * ADM not sufficient accuracy yet (needs further testing)
951    
952    checkpoint53b_post
953    o Commiting new energy balance model to repository
954      * package is pkg/ebm
955      * verif. is verification/global_ocean_ebm
956      * references are in ebm_driver.F
957    C      * X. Wang, P. Stone and J. Marotzke, 1999:
958    C        Global thermohaline circulation. Part I:
959    C        Sensitivity to atmospheric moisture transport.
960    C        J. Climate 12(1), 71-82
961    C      * X. Wang, P. Stone and J. Marotzke, 1999:
962    C        Global thermohaline circulation. Part II:
963    C        Sensitivity with interactive transport.
964    C        J. Climate 12(1), 83-91
965    C      * M. Nakamura, P. Stone and J. Marotzke, 1994:
966    C        Destabilization of the thermohaline circulation
967    C        by atmospheric eddy transports.
968    C        J. Climate 7(12), 1870-1882
969    o Will need long integration testing.
970    checkpoint53b_pre
971    
972    o created pkg/mom_common in preparation for variable viscosity code
973    o renamed and split ini_mnc_io
974    o pkg/land: only liquid water can diffuse or run-off
975    o AIM using land: soil wetness availability account for snow
976    o added printMapIncludesZeros to EEPARMS namelist
977    
978    checkpoint53a_post
979    o restore TAMC compatiility for exf_constants.h
980      (no usage of _d in .h)
981    o Additional storing in KPP in an attempt to fix
982      TAMC problem with adjoint of KPP code.
983      (no success...)
984      Identical code works fine with TAF.
985    o Fixed verification/natl_box_adjoint experiments.
986      Initial conditions for Experiments 4 and 5 are now
987      set to "SEAICE_initialHEFF=0", which is more reasonable,
988      and hence gives results closer to that of Experiment 2.
989      Experiment 6 requires "SEAICE_initialHEFF=1" and is working once again.
990    
991    checkpoint53
992    o stable checkpoint with up to date adjoint
993      TLM tests only run for 1st grdchk at the moment. Its unclear if
994      this is a code problem or a problem with resetting code for g_
995      variables that is being autogenerated wrong.
996      Otherwise:
997       o code is testing well on Linux (P4 and AMD), SGI Alitix and Irix.
998       o IBM and HPQ tests could not be run because NCAR (IBM) and NCCS (HPQ)
999         are both still in chaos following their security messes.
1000    
1001    checkpoint52n_post
1002    o various build (mostly genmake2) changes including:
1003      - ability to build/run more easily within Cygwin and MacOS X
1004      - more complicated Makefiles with a stronger dependence on Gnu Make
1005    o pkg/seaice modifications
1006      - added SEAICE_deltaTtherm and SEAICE_deltaTdyn in order to reduce cost
1007        of pkg/seaice.  For time being, SEAICE_deltaTtherm = deltaTtracer
1008        and SEAICE_deltaTdyn must be integer multiple of SEAICE_deltaTtherm
1009      - changed proxy for geostrophic velocity and updated
1010        verification/lab_sea/results/* accordingly
1011      - removed ADI dynamic solver from pkg/seaice
1012      - replaced all occurrences of 1/CSTICE or 1/CSUICE
1013        they caused a segmentation fault under certain circumstances
1014      - removed unused field WATR
1015    o bug fix in exf-package:
1016      -  u/vwind are defined at tracer/pressure points. The values of u/vwindmask
1017         now reflect that.
1018    o small fixes in the cal-package:
1019      - set reference date to first of January for the 'model'-calendar
1020      - failing of cal_CheckDate in cal_FullDate now actually results in a
1021        warning
1022    o small modifications in exf-package to increase flexibility:
1023      - change climtempfreeze from a constant to a runtime parameter that
1024        is specified in data.exf_clim (default = -1.9)
1025      - introduce runtime parameter windstressmax (default = 2.0) that is
1026        specified in data.exf
1027    o fix in pkg/thsice:
1028      - update Evap (Tsf changes) to be consistent with Latent heat flux
1029      - maintain snow precipitation unchanged (even if Tsf >=0).
1030     both affect global_ocean.cs32x15/(.thsice) results ; update output.txt.thsice
1031    
1032    checkpoint52m_post
1033    o commented out call to cal_GetMonthsRec in swfrac.F and added some comments;
1034      this does not change any of the results, because myIter=0 in swfrac always
1035      lead to jwtype=2 (the default anyway), but the call makes little sense
1036      as a default
1037    o no SHORTWAVE HEATING lost at the bottom; affects lab_sea output; updated
1038    o re-work pkg/thsice interface with ocean & bulk_force pkg to allow
1039      atmospheric model (AIM) to use it ; add a "slab ocean" component.
1040    o pkg/aim_v23 : add interface to call thermodynamic sea-ice (thsice)
1041    o update global_ocean.cs32x15/output (.thsice) after changes in pkg/thsice
1042    o extending useSingleCpuIO option to work with new exch2 I/O format
1043      - old-style, missing-tile I/O is still accessible by defining CPP
1044        option MISSING_TILE_IO in pkg/mdsio/MDSIO_OPTIONS.h
1045    o monitor package can write to NetCDF files and/or STDOUT
1046    o fix re-definition bug in MNC_GRID_INIT_ALL()
1047    o doc/api_reference added
1048      - a framework for building an API Reference Manual using all
1049        the "protex" comments embedded in the code
1050      - see pkg/generic_advdiff, pkg/mnc for examples
1051    o MNC:
1052      - make myThid the last argument for all subroutines
1053      - new default for the grid files: NO halos
1054      - add useMNC and other run-time flags
1055      - separate per-file-group handling of the unlimited dimension
1056      - early initialization of MNC w/ flags read at the eeboot stage
1057        and lookup tables set in initialize_fixed
1058      - write all MNC output to a freshly-created directory
1059    o thermodynamics sea-ice (thsice) is now tested with testreport.
1060    o test exp. advect_cs: use the standard cs32 grid ; update output.
1061    o Added functionality to grdchk:
1062      pick global i,j,k position (or nearest wet) where to perform check.
1063    
1064    checkpoint52l_post
1065    o new land formulation:
1066      a) use ground enthalpy as prognostic variable to ensure exact
1067         energy conservation.
1068      b) account for water temperature and for latent heat of freezing
1069         in all processes (rain, run-off, ground storage)
1070      c) compute surface and ground temperature implicitly.
1071    o aim_v23 modification for new land model:
1072      a) Treat separately land / ocean / sea-ice surface fluxes
1073         to allow implicit computation of land & sea-ice surface temp.
1074      b) add snow precipitation.
1075    checkpoint52l_pre
1076    
1077    o fix problem (when 1 tile is empty) in min/max monitor.
1078    o fix bug in timeAve (u,vZetatave in common block)
1079    o no restoring terms under ice for pkg/seaice
1080    o moved SEAICE_DO_DIAGS to S/R do_the_model_io
1081    o bug fix for pkg/seaice pickups
1082    o change MNC call locations and add coordinate attributes
1083    o mask vorticity at the corner ; affects global_ocean.cs output
1084    o fix ini_curvilinear_grid ; test CS experiments with mpi
1085    o aim.5l_cs: modify sea-ice fraction input file ; update output
1086    o exf: Adding simple range check routine for exf fields after read
1087    
1088    checkpoint52k_post
1089    o removed top-level directory "diags"
1090      - we migrated these functions to pkg/timeave a long time ago
1091    o fixed bug introduced in pkg/monitor
1092    o accuracy ctrlprec = 32 insuffient for gradient checks using
1093      averaged fields (I/O via cost_averages)
1094      -> use ctrl.h in active_file*.F to control I/O precision.
1095    o paramter list of CALL ADTHE_MAIN_LOOP
1096    o added initial do_the_model_io to ecco
1097    o set all ...Freq to zero after cost_final
1098      taveFreq, dumpFreq, pChkptFreq
1099    o MAIN and ECCO differentiability restored
1100    
1101    checkpoint52j_post
1102    o fix nchklev in tamc.h for global_ocean...
1103    o Bringing flow and store directives up-to-date
1104    o Really weird thing!
1105      call do_the_model_io from the_main_loop with parameters
1106      starttime, niter0, instead of mytime, myiter, screws up the adjoint:
1107      TAF places a faulty re-call of initialise_varia
1108      after cost_final call which should not be there!
1109    checkpoint52j_pre
1110    
1111    o tweaked pkg/mdsio/mdsio_readfield.F to have more useful logic and
1112      error messages
1113    o fix errorMessageUnit problem. remove old version of mdsio from eesup/src
1114    o modified pkg/mdsio/mdsio_readfield.F -- commented out diskspace-eating
1115      debug output
1116    o modfied mdsio_writefield.F to handle non-global files under exch2
1117    o update AIM Cubed-Sphere exp (aim.5l_cs):
1118      use land, p*, and Franco.M forcing fields with fractional land-sea mask.
1119    o update AIM Equatorial Channel exp:
1120      use standard aim_v23 pkg and change the SST fields to be more realistic.
1121    o globalFile now works with exch2
1122    o merged mom_vi_calc_relvort3.F, mom_vi_del2uv.F and
1123      mon_vort3.F to make exch2 friendly with >1 tile per cube face
1124    o limit timeave output for hi-res integrations
1125    
1126    checkpoint52i_post
1127    o removed CPP_EEOPTIONS.h from verification/*/code
1128    o updated the tiling for global_ocean_pressure
1129    checkpoint52i_pre
1130    
1131    o update aim.5l_LatLon using the standard aim_v23 pkg (instead of
1132      the old pkg/aim).
1133    
1134    checkpoint52h_pre
1135    o shortened offending lines in exch2_send_rx?.template
1136    o modified W2_EXCH2_TOPOLOGY.h to reflect current topology generator
1137    o genmake2: add build & execute test for NetCDF code
1138    o modded aim.5l_cs and global_ocean.cs32x15 to use exch2, removed
1139      old grid files, moved CPP_EEMACROS.h to pkg/exch2
1140    o added useSingleCPUIO flag to monitor.F and mon_out.F
1141    o added temporary hack for sea-ice dynamics on the cube:
1142      metric terms are ignored and it is assumed that
1143      there is no sea-ice on cube faces 1, 2, 4, and 5.
1144    
1145    checkpoint52f_post
1146    o added exch2 cube routines to pkg/exch2
1147    o modified hs94.cs-32x32x5 to use it
1148    o added new grid files to hs94.cs-32x32x5
1149    checkpoint52f_pre
1150    
1151    checkpoint52e_post
1152    o first attempt to solve vertical advection (momemtum & T,S) Implicitly
1153      for now, only implemented with Lax-Wendroff (tracer) and VectInv (mom)
1154    o step.1 : rewrite (as in MultiDimAdvec) explicit tracer stepping (gad_calc_rhs.F)
1155      to work with implicit vertical advection and AB ;
1156    o Implic. vert. advect. implemented with flux-limiter, c2, u3 and c4 scheme.
1157    o update output (gad_calc_rhs.F changes affect truncation error) of exp:
1158     front_relax, global_ocean .cs32x15 & _pressure, internal_wave, lab_sea, natl_box
1159    checkpoint52e_pre
1160    
1161    o fix bug in impldiff when Nr=1 or Nr=2.
1162    o change the albedo in pkg/thsice (as GISS model); update output_thsice.txt
1163    o little changes (fftpack, aim/phy_suflux ...) to pass the "checkbounds" test.
1164    o fix deltaTfreesurf in update_cg2d.F (left from c45d_post): affects 2
1165      ocean exp. that use NLFS: global_ocean.cs32x15 & global_ocean_pressure
1166    o added exf_offset_atemp for Celsius to Kelvin conversion of atemp
1167    o eesupp/inc/EEPARAMS.h: MAX_NO_PROCS=1024
1168    o pkg/cal/cal_toseconds.F fix for long (>60 years) integrations
1169    
1170    checkpoint52d_post
1171    o re-tiled many expts to allow comparison in multi-processor mode
1172      - updated output accordingly
1173      - changed hs94.128x64x5 to use intial T from file rather than use the
1174        random number generator
1175    o add infrastructure in model routines for fizhi and gridalt packages
1176    o change global_ocean.cs32x15 because of Pb with GM on CS-grid.
1177    o changes to permit hi-res, cubed-sphere, configuration
1178      - added useSingleCpuIO capability to mdsio_readfield.F and exf_interp.F
1179      - added "#undef ALLOW_USE_MPI" support to eesupp/src/scatter_2d.F
1180      - added pkg/exf/exf_set_uv.F for on-the-fly interpolation and rotation
1181        of surface winds for the cube
1182      (A verification experiment, based on global_ocean.cs32x15, but with
1183       pkg/seaice turned on and with on-the-fly interpolation from the NCEP
1184       Gaussian grid is described in MITgcm_contrib/high_res_cube/README_ice,
1185       complete with example surface forcing files and matlab scripts to look
1186       at the output and compare it with that of global_ocean.cs32x15.)
1187    o packages pickup: $PKG_write_pickup called from packages_write_pickup ;
1188       but call to $PKG_read_pickup remains in $PKG_ini_vars: change CD_code
1189       to conform to the common rule.
1190    o check-in the first version of the coupler + interfaces for multi-components
1191       set-up (Chris's version, adapted to work on cubed-sphere grid); use MPI.
1192       - imply modification in eesupp (MPI_COMM_MODEL < MPI_COMM_WORLD).
1193       - atmosphere: use pkg aim_v23 ; no sea-ice for now.
1194       - ocean and atmos. share the same horizontal grid (no interpolation).
1195       - exchanges between component and coupler is done in forward_step
1196    o new verification experiment, cpl_aim+ocn:
1197       coupled ocean - AIM atmosphere on cs32 grid.
1198    
1199    checkpoint52d_pre
1200    o surface flux time-av diagnostic modified for NLFS & RealFreshWater
1201    o add call to AIM pendant S/R in external_forcing & external_fields_load.F
1202    
1203    checkpoint52c_post
1204    o Fixing OPTIONS files for use of exf:
1205      - ALLOW_ECCO not needed
1206      - ECCO_CPPOPTIONS.h should not be included from
1207        EXF_OPTIONS.h/CAL_OPTIONS.h, but from CPP_OPTIONS.h
1208        as has been the case in the past
1209      - All cal/exf related options are currently set in
1210        single header file. Should remain so until we
1211        agree on a consistent new policy.
1212    o Removed all CPP options for cal package.
1213      cal has no more CPP options.
1214    o modified STOREs in GAD_ADVECTION
1215    o corrected key comp. for passkey
1216    
1217    checkpoint52b_post
1218    o new version: "thsice" of thermodynamic sea-ice pkg:
1219     - only 1 call from "forward_step"; conserve energy, fresh-water & salt.
1220     - modify fluxes but do not change theta directly;
1221     - light cleaning of bulk_force pkg (still needed with thsice).
1222     - add forcing fields + data files in global_ocean.cs32x15/inp_thsice
1223       + output_thsice.txt to test thsice & bulk_force pkgs.
1224    o put back grid & coriolis monitor output.
1225    checkpoint52b_pre
1226    
1227    o call "do_the_model_io" at the beginning (=> dump initial state)
1228    o use rhoConstFresh to define convertEmP2rUnit (was done only in ocean-P)
1229    o sort out interplay between tamc.h and PTRACERS_OPTIONS.h
1230      (need info on NUMBER_OF_PTRACERS)
1231    o missing PTRACERS headers in some routines
1232    o default tamc.h in pkg/autodiff supposed to crash
1233      to ensure proper customization
1234    
1235    checkpoint52a_post
1236    o modifications to make FREEZE (_SURFACE) flux visible to pkg/kpp
1237      - moved surfaceTendencyTice from pkg/seaice to main code
1238      - subroutine FREEZE_SURFACE now limits only surface temperature
1239        and is called in FORWARD_STEP (if allowFreezing=.TRUE.)
1240        => new output.txt for global_ocean.cs32x15 & global_with_exf
1241      - keep the old version of FREEZE for backward compatibility;
1242        global_ocean.90x40x15 left unchanged using useOldFreezing=.TRUE.
1243      - corresponding modifs for TAF directives
1244    o added surface flux output variables to TIMEAVE_STATVARS
1245    o time-averaged output for pkg/ptracers
1246    o fix problem with ECCO-related divided adjoint
1247      snapshot file was missing some ad-variables,
1248      but no warning issued by TAF
1249    
1250    checkpoint52a_pre
1251    o some bug fixes for #undef REAL4_IS_SLOW
1252    
1253    checkpoint52 = ecco_c52_e35
1254    o after testing adjoints of checkpoint51u_post
1255    
1256    checkpoint51u_post
1257    o this is the post-merge tag of the ecco-branch
1258      (needs another clean checkout and re-testing)
1259    o various natl_box_adjoint configs and results
1260      but no input fields
1261    o obcs adjoint not yet merged!
1262    o adding ECCO global 1x1 and 2x2 degree configs
1263    o updated/extended some store directives for seaice
1264    o pkg/ecco now containes ecco-specific part of cost function
1265    o top level routines the_main_loop, forward_step
1266      supersede those in model/src/
1267      previous input data.cost now in data.ecco
1268      (new namelist ecco_cost_nml)
1269    o in ctrl/ cleaned some cross-dependencies and updated CPP options
1270    
1271    checkpoint51t_post
1272    o this is the pre-merge tag of the ecco-branch
1273    
1274    checkpoint51s_post
1275    o cleanup: removed various obsolete #define-s
1276    o pkg/grdchk
1277      - renamed 'ph-grd 3' to 'grad-res'
1278      - merged from ecco-branch
1279        (remaining bug fixes for obcs gradient checks)
1280      - additional high-precision output for testreport
1281        (grep for 'precision_grdchk_result')
1282    
1283    checkpoint51r_post
1284    o cleaned up or removed CPP_OPTIONS.h files
1285    o updated results for some of the tests to reflect the new
1286      optfiles (-ieee: -O0 instead of -O3)
1287    
1288    checkpoint51q_post
1289    o cd_code:
1290      - moved cd_scheme.F -> cd_code_scheme.F
1291      - separate read_checkpoint from cd_code_ini_vars.F
1292      - separated cd_code part from write_checkpoint
1293      - updated AD_SOURCE, generated .flow
1294      - added CD_CODE_VARS.h to the_main_loop
1295      - Moving cd_code specific store dir.s to pkg/cd_code
1296    o ctrl package totally restructured
1297      - pack/unpack now optional and decoupled from
1298        xx_/adxx_ I/O
1299      - ctrl_pack/unpack cleaned
1300        (new routines ctrl_init_ctrlvar.F, pkg/ctrl/ctrl_init_wet.F)
1301      - confined inclusion of AD_CONFIG.h to where necessary.
1302    o genmake2: changed AD dependencies from SRCFILES to AD_FILES
1303    
1304    checkpoint51p_post
1305    o create initial cd_code package
1306      - WARNING: the initialization of fields within packages
1307        is broken because INI_FIELDS (where READ_CHECKPOINT is
1308        called) is called *before* PACKAGES_INIT_VARIABLES.
1309        This seems to be backwards since
1310        1) its important to initially zero the entire field including
1311           the "halo" region
1312        2) zeroing needs to be done *before* reading pickup info
1313           and the pickup call might or might not happen in any
1314           particular run
1315      - this needs an overhaul for R2
1316    o cleanup verification/*/code/GMREDI_OPTIONS.h
1317    o cleanup testreport
1318    
1319    checkpoint51o_post
1320    o bringing AD-related verif's up to date with genmake2
1321      - carbon/
1322      - global_ocean.90x40x15/
1323      - hs.94.1x64x5/
1324      - (front_relax/ )
1325    o (more) consistent directory structure for AD-related verif.'s
1326    o cleaning ALLOW_GRADIENT_CHECK -> ALLOW_GRDCHK
1327    o cleaning some ALLOW_TANGENTLINEAR_RUN -> ALLOW_AUTODIFF
1328    o bug fix in find_alpha.F for MDJWF:
1329      - modif. to alpha = 1/D*( dN/dT - rho*dD/Dt) to account for
1330        change rho -> rho-rhoConst
1331      - replace call find_rho to find_rhonum
1332    o initialisation of rFlx extended to full array (required by TAF)
1333      and shifted to thermodynamics
1334    o removed PTRACERS.h in ptracers routine
1335    o added surfacetendencyPtr to S/R parameter list pracers_forcing
1336    o Correcting initialisations for fVerU, fVerV.
1337    o helping TAF to recognize dependency on kUp for
1338      fVerU, fVerV
1339    o Replacing delZ by delR in pkg/ctrl/
1340    checkpoint51o_pre
1341    
1342    o undid all of cp51 pending some cleanups and discussion
1343    o added the [#include "AD_CONFIG.h"] statement to all files that need
1344       it for adjoint/tl #defines
1345     o re-worked the build logic in genmake2 to support AD_CONFIG.h
1346     o removed tools/genmake since it no longer works
1347    
1348    checkpoint51n_post
1349    o modifications to make FREEZE flux visible to pkg/kpp
1350      - moved surfaceTendencyTice from pkg/seaice to main code
1351      - FREEZE & EXTERNAL_FORCING_SURF moved to FORWARD_STEP
1352      - subroutine FREEZE now limits only surface temperature
1353        (this means new output.txt for global_ocean.90x40x15,
1354         global_ocean.cs32x15, and global_with_exf)
1355    o added surface flux output variables to TIMEAVE_STATVARS
1356    
1357    checkpoint51n_pre
1358    o added "#undef ALLOW_USE_MPI" support to eesupp/src/gather_2d.F
1359    o added [#include "AD_CONFIG.h"] to all files that use the following
1360      defines:
1361      - ALLOW_ADJOINT_RUN
1362      - ALLOW_TANGENTLINEAR_RUN
1363      - ALLOW_ECCO_OPTIMIZATION
1364    
1365    checkpoint51m_post
1366    o incorporating changes to get TAMC/TAF working in genmake2
1367      - added new TAMC/TAF targets to the Makefile
1368      - various cleanups related to package handling
1369      - these changes should have no impact on the forward model
1370    
1371    checkpoint51l_post
1372    o changes to pkg/cal and pkg/exf that allow and speed-up long integrations
1373     - faster algorithm for cal_addtime.F
1374     - higher precision arithmetic, where needed
1375     - pkg/exf *startdate variables changed from calendar date to
1376       model integration time
1377    
1378    checkpoint51l_pre
1379    o add salt flux to forcing fields (used when salty sea-ice forms or melts)
1380    o enable to apply restoring on S & T only in a latitude band.
1381    o update output (external_forcing_surf modif. change truncation errors)
1382       global_ocean.cs32x15, global_ocean_pressure, lab_sea, natl_box
1383    
1384    checkpoint51k_post
1385    o change default to: useNHMTerms=.FALSE.
1386     - new output.txt for atmos. exp (NHMTerms were wrong but now turned off):
1387       adjustment.128x64x1, aim.5l_Eq_Ch, aim.5l_LatLon, hs94.128x64x5, hs94.1x64x5
1388     - new output.txt for idealized oceanic exp (NHMTerms are now turned off):
1389        exp1, ideal_2D_oce
1390     - change data file of oceanic exp (leave the results unchanged for now)
1391       exp2, global_ocean[90x40x15,pressure,with_exf], lab_sea, natl_box
1392    o set gravitySign automatically according to the vertical coordinate used
1393      (and change sign: back to "logical" value: +1 when R increases downward)
1394    o added an include barrier to the default CPP_OPTIONS.h and
1395      removed the #include "PACKAGES_CONFIG.h" from it
1396    o fix a bug in mom_fluxform (from chk51j_post)
1397    
1398    checkpoint51j_post
1399    o Added some AD-related initialisations in mom_vecinv/ mom_fluxform/
1400    o adjusted some flow directives (dynamics, thermodynamics)
1401    o added cubed-sphere case to test cost function
1402    o heckpoint_lev?_directives.h now include
1403      pkg-specific directives, whenever those are enabled.
1404    o Moving pkg-specific flow directives to corresponding pkg
1405      Moving pkg-specific differentiation list to corresponding pkg
1406      Moving pkg-specific checkpoint-lev storing to corresponding pkg
1407      ---> conventions are
1408           - pkg_ad.flow
1409           - pkg_ad_diff.list
1410           - pkg_ad_check_lev?_dir.h
1411    
1412    checkpoint51i_post
1413    o merge of the branch-genmake2
1414      - knowingly breaks the older genmake
1415      - automatic generation of all ALLOW_${PKG_NAME} defines
1416      - new testreport supersedes older testscript
1417    o large number of package inclusion and header cleanups
1418    checkpoint51i_pre
1419    
1420    o new output for adjoin of global ocean vector invariant
1421    o fix for checkpoint of thermodynamic seaice and bulk_force
1422    o Steph gchem various cleanups
1423    
1424    checkpoint 51h_pre
1425    o fixed some single quotes
1426    o modify gchem pkg to be more versatile
1427    o modifications to clean up dic pkg
1428    o add pkg/cfc
1429    
1430    checkpoint51g_post
1431    o provide links for ARPACK and ADM*TLM
1432    o start removing verification/vero/
1433    o update AD-related stuff
1434      (in particular some IF-statements in model/src/ routines)
1435    o adding to verification/global_ocean.90x40x15/ adjoint of
1436      vector invariant setup
1437    
1438    checkpoint51f_post
1439    o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
1440    o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
1441      of tracer Green's fucntions for ocean inversion project.
1442    
1443    checkpoint51f_pre
1444    o Added on-the-fly spatial interpolation capability
1445        "USE_EXF_INTERPOLATION" to pkg/exf.
1446      - This is a temporary Cartesian-grid hack until
1447        the super-duper ESMF coupler becomes available.
1448      - See verification/global_with_exf/README for usage example.
1449      - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
1450        flags and modified pkg/seaice accordingly.
1451    o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
1452        and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
1453        non-local transport term.
1454    
1455    checkpoint51e_post
1456    o pkg/mom_vecinv:
1457      - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
1458      - add time-ave diagnostic of vorticity advection.
1459    o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
1460    o atmospheric geopotential: - include water vapor effect;
1461                                - use p^kappa in p* scaling.
1462    o land pkg: read initial state from files.
1463    o AIM : add stratospheric drag in the upper level
1464    
1465    checkpoint51d_post
1466    o change function ILNBLNK (=> last non-blank char.) to return zero
1467      (instead of the string length) when the string. char is empty
1468    o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
1469    o modif's to restore TAMC compatibility
1470      - avoid "_d" constructs in PARAMETER declarations
1471      - avoid interrupting lines by comment lines
1472    o Use cluster local disks for purely local I/O
1473      vs. globally visible disks needed for ctrl stuff
1474      (merged from ecco-branch)
1475      - new active_file_loc... and mdsio_..._loc routines
1476      - affected packages: autodiff, ctrl, grdchk, mdsio
1477    
1478    checkpoint51c_post
1479    o introducing integer flag debugLevel
1480      - debLevZero: suppress all output
1481      - debLevA: standard
1482      - debLevB: equivalent to current debugMode=.TRUE.
1483    o introducing pathname variable mdsioLocalDir for mdsio
1484      that can be specified at runtime
1485      (relevant for cluster I/O to local disk)
1486    `
1487    >>>checkpoint51b_post
1488    adjoint of ptracers
1489    o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
1490    o extended state in checkpoint_lev?, etc.
1491    o alternative ctrl/cost with tr1 or ptracer
1492    o new comlev1_bibj_ptracers
1493    o new ptracers.flow
1494    o made ptracers_forcing same as external_forcing_s
1495    o added verification for adjoint with ptracers
1496      - adm. grdchk fail so far
1497      - tlm. grdchk OK
1498      - checked tapelev/comlev recomputations: OK
1499    <<<checkpoint51b_pre
1500    
1501    checkpoint51a_post
1502    o added code for biogeochemistry package
1503      - new pkgs: dic, gchem
1504      - new subroutine in ptracers
1505    o modify code for biogeo packages
1506      - in model/src and pkg/ptracers
1507    
1508    checkpoint51
1509    o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
1510      - autodiff, ctrl, exf, grdchk, seaice
1511      kept separate packages
1512      - cost, ecco, obcs
1513    o updating verification/internal_wave, verification/lab_sea
1514      (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
1515    
1516    checkpoint50i_post
1517    o Preparing next differentiable checkpoint and sync
1518      of MAIN vs. ecco-branch
1519      - 1st step: this one is differentiable
1520      - 2nd step: next(! not this) checkpoint will have updated packages
1521                  from ecco-branch)
1522    
1523    checkpoint50h_post
1524    o new package "land": provide surface BC for AIM.
1525    o pkg/ptracers: apply exchange to all tracers after reading a pickup.
1526    o AIM: use true log-P extrapolation for near surface temp (= as in
1527        F.Molteni paper) ; update aim.5l_cs output.
1528    o New variable in PARM03 for more flexible pickups
1529    o somewhat cleaned package initialisation sequence for
1530      ctrl/ cost/ ecco/ in packages_... routines
1531    
1532    checkpoint50g_post
1533    o merged with release1_p17 (pkg/seaice and verification/lab_sea)
1534      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
1535      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
1536        made the default because of faster convergence than ADI
1537    
1538    checkpoint50f_post
1539    o exf totally restructured
1540      - replaced all exf_set_ routines by one generic exf_set_gen.F
1541        and made sure it's still differentiable
1542      - split exf_getffields.F into new exf_bulkformulae.F
1543      - exf_inscal_/exf_outscal_ suffixes consistent with field names
1544      - updated adjoint/makefile and relevant verif. accordingly
1545    
1546    checkpoint50f_pre
1547     o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
1548          + change Evap over land. (update aim.5l_cs output)
1549     o added missing .cvsignores and made uniform across expts
1550     o changed configuration of tidal_basin_2d expt
1551     o added pkg/debug functions for tracing code in fatal crashes
1552     o tidied pkg/monitor to use MONITOR_OPTIONS.h
1553     o new fn in pkg/monitor to stop model if solution grows too big
1554     o removed lots of single quotes from comments
1555    
1556    checkpoint50e_post
1557    o make KPP work with PTRACERS
1558     - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
1559       nearly a copy of kpp_transport_s
1560     - there is no analogue to SurfaceTendencyS, so I have to use
1561       gPtr(of the surface layer) instead
1562    o add a new platform SunFire+mpi (SunFire 15000) to genmake
1563    checkpoint50e_pre
1564    
1565    checkpoint50d_post
1566    o change kpp output from multiple-record state files to single-record state
1567      files analogous to write_state.F
1568    o reduce the output frequency of cg3d-related stuff to the monitor frequency,
1569      analogous to the cg2d-related output.
1570    o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512,
1571      so that writing to internal file fn (with length 512) fails.
1572    checkpoint50d_pre
1573    
1574    checkpoint50c_post
1575    o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
1576    o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
1577    o add time-average diagnostic of U*V and vertical diffusive flux for theta.
1578    o bug fixed in convective adjustment diagnostic (multi-tile set-up).
1579    o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
1580    
1581    checkpoint50c_pre
1582    Merging from release1_p13:
1583    o bug fix for pkg/seaice dynamic solver
1584    o Added SEAICE_initialHEFF to pkg/seaice
1585    
1586    checkpoint50b_post
1587    o store u*,v* in gU,V instead of in guNm1,gvNm1
1588    o in order to put the momForcing out of the Adams-Bashforth:
1589      move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
1590      to timestep.F
1591    o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
1592    o re-generate output for highly sensitive test-exp:
1593       global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
1594    
1595    checkpoint50b_pre
1596    o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
1597    o corrected CPP option mismatch in exf_Bulk... functions for case
1598      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
1599    
1600    checkpoint50a_post
1601    o Bug fix for merging between c50 and KPP.
1602      ikey was passed from thermodynamics to kpp_calc via
1603      common block rather than being recomputed in kpp_calc,
1604      in contradiction with new key itdkey.
1605      New key ikppkey created, and tamc.h headers updated.
1606    
1607    checkpoint50
1608    - 2nd step of merge with ecco-branch:
1609      merge changes in ecco-branch back into main trunk
1610    - bug fix in find_alpha
1611    - more storing in gmredi_calc_tensor.F, kpp_routines.F
1612    - avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
1613    - merged some sliced AD support routines
1614    
1615    checkpoint49
1616    merged from ecco-branch:
1617    o exf:
1618      - Enable initialisation of forcing fields to constant
1619        (runtime) values.
1620      - in exf_getffields.F
1621        Reduce i-/j-loop to interior domain, discarding overlaps.
1622        That also fixes wrong TAF-key computations for key_1, key_2
1623        with bulf formulae.
1624      - exf_init.F modify #ifdef for exf_init_evap
1625      - exf_getffieldrec.F, ctrl_getrec.F
1626        The following INT-usages are not safe:
1627          fldsecs  = int(fldsecs/fldperiod)*fldperiod
1628          fldcount = int(fldsecs/fldperiod) + 1
1629        and were modified.
1630    o autodiff: checkpoint_lev...
1631      - updated storing for bulk formulae (some arrays were missing)
1632      - added state for seaice package
1633      - synchronized with main branch
1634    o DIVA:
1635      Modif.s in
1636      - the_main_loop.F
1637      - the_model_main.F
1638      and added cost_final_restore.F cost_final_store.F
1639      o With these changes, it is possible to fully separate
1640        the first forward run to compute the cost function (mdthe_main_loop)
1641        and adjoint runs over individual DIVA intervals (adthe_main_loop)
1642        into separate model executions.
1643        This enables better tuning of DIVA to given queue sizes.
1644      o Loss of cost function value in consecutive DIVA runs is
1645        fixed by storing to 'costfinal' file.
1646      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
1647        beginning/end of adjoint integration is accounted for.
1648      The current changes apply to TAF-1.4.26.
1649      TAF has one remaining bug, requiring one manual change
1650      (see MITgcm manual).
1651    o cal: synchronized between MAIN and ecco-branch
1652    
1653    checkpoint48i_post
1654    o Changes to restore differentiability of code w.r.t. previous tag
1655      (mostly adding new routines to make list and replacing
1656      pressure by totPhiHyd).
1657    o Updated and merged grdchk package
1658      - has both ADM and TLM checks
1659      - works for single- and multi-proc.
1660      - output cleaned
1661      - worked successfully for parallel DIVA
1662    o genmake:
1663      - Adding -platform=SP4
1664      - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
1665    o Modif. for DIVA:
1666      ctrl_unpack should not be called in intermediate DIVA interval.
1667      (similar thing would apply for active files such as
1668      tbar, sbar, psbar, which should not be reinitialised;
1669      only relevant for ecco-branch)
1670    
1671    checkpoint48h_post
1672    o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
1673    o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
1674    o Added SEAICE_initialHEFF to pkg/seaice
1675    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
1676    
1677    checkpoint48g_post
1678    --- EOS:
1679    o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
1680      store total Potential in totPhyHyd for diagnostics & EOS.
1681    o fix restart and overlap Pb when using Z-coord and EOS funct. of P
1682    --- Pressure/geopotential gradient:
1683    o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
1684    o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
1685      ( changes results of global_ocean_pressure )
1686    o NLFS + z-coord.: add eta*Rho' contribution.
1687    o accurate phiHyd when using interface-W at the middle between 2 centers
1688     ( changes results of ideal_2D_oce )
1689    o includes r* 2nd term in potential gradient.
1690    
1691    checkpoint48f_post
1692    Merging from release1_p12:
1693    o Modifications for using pkg/exf with pkg/seaice
1694      - improved description of the various forcing configurations
1695      - added basic radiation bulk formulae to pkg/exf
1696      - units/sign fix for evap computation in exf_getffields.F
1697      - updated verification/global_with_exf/results/output.txt
1698    o Added pkg/sbo for computing IERS Special Bureau for the Oceans
1699      (SBO) core products, including oceanic mass, center-of-mass,
1700      angular, and bottom pressure (see pkg/sbo/README.sbo).
1701    o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
1702      to avoid negative values in shallow regions.
1703      - updated verification/natl_box/results/output.txt
1704      - updated verification/lab_sea/results/output.txt
1705    o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
1706    o Added useSingleCpuIO option (see PARAMS.h).
1707    o Updated useSingleCpuIO option in mdsio_writefield.F to
1708      work with multi-field files, e.g., for single-file pickup.
1709    o pkg/seaice:
1710      - bug fix in growth.F: QNET for no shortwave case
1711      - added HeffFile for specifying initial sea-ice thickness
1712      - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
1713    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
1714      kpp_transport_t.F, forward_step.F, and the_main_loop.F
1715    o pkg/seaice:
1716      - adjoint-friendly modifications
1717      - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
1718    
1719    checkpoint48e_post
1720    o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
1721    o dynamics: change definition of computational domain & adapt mom_fluxform
1722      accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2.
1723    o following exp works with Olx=Oly=2 (and pass through checkbounds option):
1724        adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
1725        exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
1726        global_ocean.90x40x15 global_with_exf global_ocean_pressure
1727        inverted_barometer solid-body.cs-32x32x1
1728      (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
1729    
1730    checkpoint48d_post
1731    o in preparation for r*:
1732     a) use pre-computed gradient of hydrostatic potential:
1733        changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
1734     b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
1735        => affects results of glob_oce_pressure (different truncation error)  
1736      update output.txt of ideal_2D_oce & global_ocean_pressure
1737    
1738    checkpoint48d_pre
1739    o in preparation for r*:
1740      new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
1741      pass the 2 comp. of the grad. as arguments to momentum S/R.
1742      but for the moment, only used if it does not change the results.
1743    o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
1744    
1745    checkpoint48c_post
1746    Modifications in treatment of initial flux forcing controls
1747    to avoid extra storing of flux fields.
1748    
1749    checkpoint48c_pre
1750    o Added tidal_basin_2d experiment (currently 1D!)
1751    o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented)
1752    
1753    checkpoint48b_post
1754    o r* coordinate added in #ifdef NONLIN_FRSURF block.
1755     (modification to pressure gradient not yet implemented)
1756    o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
1757      (for U & V) that are used for vertical advection of momentum.
1758    
1759    checkpoint48a_post
1760    o In preparation for r*, use temp. array to compute vertical transport
1761       in flux-form momentum pkg. => change results of few test-exp.
1762      Update output of: exp4, exp5, front_relax, global_ocean_pressure,
1763                        lab_sea, natl_box & plume_on_slope
1764    
1765  checkpoint48  checkpoint48
1766  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')  o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
1767    

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